Flagstaff-based TGEN solves medical mysteries

FLAGSTAFF – After Flagstaff hospital officials noticed an unusual increase in the number of strep throat patients, they requested assistance from the Translational Genomics Research Institute in Flagstaff.

The health officials wanted to determine the strain so they could better treat and prevent the illness.

The nonprofit institute, also known as TGen North, solved the mystery by looking at the genomes of those infected – and it turned out the culprit evolved from a “superbug.” The institute’s Pathogen Genomics Division also helped figure out the source of illness among child cancer patients in Chile by identifying a fungus in their medication, according to a study released by TGen in March.

Health departments – both locally and internationally – have utilized the institute more because of its technology and expertise. Most of the time when looking at genomes, the TGen team comes up empty-handed. So when they make a definitive identification like they did in Flagstaff, it can create a big change in the care for patients affected.

“We definitely see being a part of the public health system as a part of our mission. The pressure’s on,” said David Engelthaler, director of programs and operations at TGen North, and the lead author of the study. “It drives us and we’re proud to be able to have the capabilities to provide this resource to the state and national and international public health systems.”

Strep throat in Flagstaff

The institute’s scientists took apart strands of DNA and separated their portions or “islets” to compare their sequences to normal strands of DNA to check for mutations.

After observing six genome strains, the TGen team identified that the patients had an emm59 type of strep throat called group A streptococcus. The bacteria that causes this strain of strep throat can develop into necrotizing fasciitis in wounds, something the Centers for Disease Control and Prevention calls a “flesh-eating infection” that can result in a loss of limb or even death.

“We worked directly with the hospital, and we were able to get strains of the ‘group A’ strep, do the analysis and prove that there was an outbreak going on,” Engelthaler said.
“At that point, we brought in public health, both county and state public health, to assist with the investigation.”

This strain of strep throat is thought to be evolved from an outbreak several years ago in Canada, and Engelthaler refers to as a “superbug.” The same bug also was identified in patients in New Mexico.

The hospital can now use specialized treatment for the patients.

“On one level, we hope the impact will be to eventually see fewer group A streptococcal disease cases,” said Mare Schumacher, Coconino County Public Health Services Department epidemiologist. “Perhaps as importantly, we hope that cases of group A streptococcal disease are treated quickly and properly.”

Schumacher said now that they have identified the strain, they hope to prevent the spread in two ways.

“First, we are promoting hand washing, good care of wounds and staying home when you are sick,” Schumacher said. “This is somewhat difficult because the group A streptococcus bacteria are everywhere.”

They also plan to prevent the spread by treating wounds quickly at hospital.

Other applications

Genomic sequencing is just one of the tools that TGen has in its belt.

“Sometimes it’s helping solve disease outbreaks, both locally and internationally, but sometimes it’s developing new diagnostic tools or new monitoring tools for bio defense, or creating tools that go to the hospitals or the health care systems to help better identify infections,” Engelthaler said.

Engelthaler, who’s worked with the institute since 2006, said that the strep throat project and the pediatric cancer projects were some of the most rewarding that the team of 35 has worked on.

“We work on a number of different investigations and a number of different (research projects) and experiments, and a lot of the time, maybe most of the time, you don’t have a satisfactory answer,” Engelthaler said. “It just leads to more questions. When you’re able to find a solution and you can help stop an outbreak or help raise awareness or help physicians better treat patients, it’s clearly rewarding and certainly, I think for all of us, it’s definitely very exciting.”